A virus is a disease
causing agent consisting of a nucleic acid molecule and protein coat. Viruses
are incapable of autonomous replication and have to use a host cell's
translational system. A bacterium
is a prokaryotic cell with its own circular DNA. A bacteriophage is a
virus that infects bacteria only. Viruses would appear to be the
simplest infectious particle. The discovery of viroids, nucleic acid without a protein
capsule and prions,
infectious proteins, subtracts another level of complexity. Both viroids and
prions can cause diseases.

Properties of Viruses

They can be morphologically variable and even complex. Their morphology is
one way of classifying viruses. They contain DNA or RNA but never both.
Although they have a protein coat around their hereditary material, they lack
properties of cells such as membranes, ribosomes, enzymes and ATP synthesis
ability. Thus, they can only proliferate by using a host cell's translational
machinery. In other words, they are obligate intracellular parasites. Their
replication cycle consists of attachment and entry into the cell; replication
of viral nucleic acid; synthesis of viral proteins; and finally, assembly of
viral components and escape from host cells. Since a virus is not a living
cell, they are neither prokaryotes nor eukaryotes. Viruses are widely used as
vectors in gene therapy.

Properties of
Bacteriophages

They have a simple structure, which consists of their double-stranded DNA
and protein coat. Only the DNA enters into the bacteria. Bacterial RNA
polymerase is composed of five individual polypeptide subunits (a2, b, b', s). The s (sigma)
factor is responsible for initiating transcription by recognizing bacterial
promoter DNA sequences. Some phages supply their own s factors to instruct the bacteria to transcribe phage genes
preferentially. They are virtually viruses but can only infect bacteria.
Bacteriophages usually infect only one species of bacteria but there are some
who can infect several species even in different genera. Their life cycle may
be either lytic (virulent phage) or lysogenic (temperate phage). Their DNA may
be integrated into the host chromosome and remain as a prophage. Integration is
achieved by recombination between a 15 bp sequence called att (for attachment) in
the host chromosome and an identical sequence in the phage chromosome. This
recombination requires an integrase (Int) enzyme encoded by the phage.
Bacteriophages are used for DNA cloning in molecular biology. DNA fragments can
be inserted into a phage and following transfection of a competent bacteria,
many copies of the desired DNA fragment can be obtained.

Properties of
Bacteria

A bacterium has four types of genetic material: its single (haploid),
covalently closed, circular dsDNA chromosome (in a supercoiled state); a
plasmid(s); a bacteriophage or prophage; and a transposon. Genetic exchange
between bacteria can occur by transfection, transduction or conjugation.
Conjugation involves F+ male bacterium and F- female bacterium. Bacteria are
haploid, but following a gene transfer (such as conjugation), they can be
partially diploid (merozygote). This may result in a double cross-over event
between the circular DNA and the linear newly introduced DNA if the two copies
of the DNA are related. Sexual reproduction and meiosis do not occur in
bacteria but genetic recombination to increase diversity is still possible by
horizontal gene transfer (see below).

While bacteria are haploid organisms, plasmids
can be considered as additional mini-chromosomes. Plasmids can be 1 to 300 kb
long and may exist as multiple, free copies in a bacterium. As a rule, small
plasmids occur in multiple copies per cell (high copy number), and large
plasmids have a low copy number. Plasmids cannot replicate outside a bacterium.
More than one types of plasmids can co-inhabit the same bacterium. Up to 10 kb
(on average 3 kb) long DNA fragments can be inserted into a plasmid. They can
enter the cells in two ways: vertical (via cell division - binary fission) or
horizontal transmission (bacterial gene swapping). Some plasmids may contain
genes that confer an evolutionary advantage to their hosts. These can be
anti-bacterial toxins, catabolic enzymes (to use unusual carbon sources), virulence
factors (pathogenic toxins), enzymes to degrade toxic compounds (like
polychlorinated biphenyls, pesticides) and most importantly, antibiotic
resistance (conferred by R plasmids). Sometimes, they may confer resistance up
to five antibiotics at the same time. Plasmids can be exchanged between
unrelated bacteria. This is the reason for speedy spread of antibiotic
resistance among them.

Sometimes, a bacterium also contains a prophage as an inserted DNA fragment
into its chromosome and this additional genetic material may be beneficial for
it. For example, a prophage of the bacterium Corynobacterium diphtheriae
carries a gene that encodes the diphtheria toxin causing the disease. Temperate
phages may exist in a bacteria in a non-replicating, latent state (prophage).
Naturally, every time a bacteria divides (every 15 to 20 minutes), the prophage
will also be replicated.

Transposable elements cannot exist as free particles in bacteria. They are integrated
in the bacterial genome or into the genetic material of a plasmid or a
prophage. They have the ability to move between these sites using an enzyme
called transposase. Transposons may also encode proteins that are useful for
bacteria (such as antibiotic or heavy metal resistance factors).

Transformation involves the uptake of DNA from the environment. Cells that
are able to take up DNA are called competent. While some bacteria (H.
influenzae, B. subtilis) are naturally competent owing to some surface proteins
they possess, others can be made competent by various treatments (calcium
chloride treatment or electroporation). This kind of transformation is an
important method used in genetic engineering.
Bacteria can take up DNA from other bacteria in nature (potentially from
genetically modified bacteria) but the fate of such DNA is usually degradation.
Historically, the principal application of transformation experiments was
genetic mapping studies on naturally competent bacteria (co-transformation
frequencies are inversely related to map distances).

Transduction involves the transfer of bacterial DNA by means of a phage
particle. Here, a desired piece of DNA is packaged into the bacteriophage head.
The bacterial DNA (which can be an entire plasmid) can be transferred to a new
cell when it is infected by the phage particle. In specialized transduction,
the genome of a temperate phage (such as l)
integrates as a prophage into a bacterium's chromosome usually at a specific
site. In generalized transduction, it is not a specific DNA segment but
whatever DNA has been loaded into the phage is transferred. For example, the m and P1 phages of E.coli can achieve
generalized transduction. Transduction can also be used to establish gene order
and for mapping purposes (only closely spaced genes will show co-transduction).
In nature, a phage may transfer parts of bacterial DNA from one bacterium to
another.

In conjugation, a direct contact
between a male (carrying a fertility factor, or F+) and a female (F-) bacteria
results in a one-way genetic material transfer (from male-to-female).
Gram-negative bacteria (like E.coli) use a physical bridge called (sex) pilus
(encoded by a conjugative plasmid) for gene transfer in conjugation, whereas,
gram-positive bacteria (like pneumococcus) use a protein called clumping factor
to get together. Some phage use the pili as receptors to attach to the
bacteria. During conjugation in E.coli, the F factor (which is a conjugative
plasmid) is not lost from the donor as it is only one of the strands of the
plasmid that has been transferred. Subsequent replications of the bacteria
restore the double-stranded state of the plasmid. When a conjugative plasmid
initiates conjugation, other plasmids can be transferred (this is called
mobilization). Conjugation is the exception to the rule that bacteria reproduce
asexually. Although conjugation resembles sexual reproduction, an important
difference is that conjugation is a one-way process. The F factor may exist as
a free plasmid or may be inserted into the bacterial genome. Some conjugative
plasmids (like the F factor of E.coli) can achieve transfer of chromosomal
genes. An E.coli strain that has this property is called Hfr strain (for high
frequency recombination). It is important to know that chromosomal genes are
transferred before the plasmid itself. If the bridge is broken during transfer,
the recipient will remain F-. Controlled conjugation experiments can be used
for gene mapping. Indeed, this approach was used to show the circularity of the
E. coli chromosome and to determine the location of 1900 of its genes.
Transformation, transduction and conjugation are means of horizontal gene
transfer in nature (see Bacterial
Gene Swapping in Nature by RV Miller. Scientific American 1998
(January), pp.47-51).